removed unused copy constructors and comments within comments that where causing...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 20a7b5235029b6d7908ca0f23f119c3c38d095f1..25e534e43880497955512ce7dc2240adf99157e9 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -212,8 +212,8 @@ void MothurOut::mothurOut(string output) {
                        if (pid == 0) { //only one process should output to screen
                #endif
                
-               cout << output;
                out << output;
+        logger() << output;
                
                #ifdef USE_MPI
                        }
@@ -234,8 +234,8 @@ void MothurOut::mothurOutEndLine() {
                        if (pid == 0) { //only one process should output to screen
                #endif
                
-               cout << endl;
                out << endl;
+        logger() << endl;
                
                #ifdef USE_MPI
                        }
@@ -257,13 +257,15 @@ void MothurOut::mothurOut(string output, ofstream& outputFile) {
                if (pid == 0) { //only one process should output to screen
 #endif
                        
-                       cout << output;
+                       
                        out << output;
                        outputFile << output;
+            logger() << output;
                        
 #ifdef USE_MPI
                }
 #endif
+        
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "MothurOut");
@@ -280,9 +282,9 @@ void MothurOut::mothurOutEndLine(ofstream& outputFile) {
                if (pid == 0) { //only one process should output to screen
 #endif
                        
-                       cout << endl;
                        out << endl;
                        outputFile << endl;
+            logger() << endl;
                        
 #ifdef USE_MPI
                }
@@ -726,7 +728,7 @@ string MothurOut::getFullPathName(string fileName){
                                        }else if (path[(pos-1)] == '/') { //you want the current working dir ./
                                                path = path.substr(0, pos);
                                        }else if (pos == 1) { break;  //you are at the end
-                                       }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
+                                       }else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
                                }
                        
                                for (int i = index; i >= 0; i--) {
@@ -772,7 +774,7 @@ string MothurOut::getFullPathName(string fileName){
                                        }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
                                                path = path.substr(0, pos);
                                        }else if (pos == 1) { break;  //you are at the end
-                                       }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
+                                       }else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
                                }
                        
                                for (int i = index; i >= 0; i--) {
@@ -1151,7 +1153,7 @@ vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& n
                                        while(isspace(d) && (d != in.eof()))            { d=in.get(); count++;}
                                }
                                positions.push_back(count-1);
-                               cout << count-1 << endl;
+                               //cout << count-1 << endl;
                        }
                        in.close();